Contacts of the helix formed by residues 35 - 44 (chain E) in PDB entry 2X2D
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 35 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E VAL* 5.6 0.9 - - - -
30E LYS* 4.2 21.6 - - + +
33E SER* 2.7 35.2 + - - +
34E PRO* 1.3 77.8 - - + +
36E VAL* 1.3 60.3 + - - +
37E ILE 3.3 0.9 + - - -
38E PRO* 3.4 16.6 - - - +
39E MET* 3.5 18.3 + - + +
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Residues in contact with VAL 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E TRP* 4.1 10.5 - - + -
26E VAL* 4.5 15.9 - - + +
27E VAL* 5.2 2.2 - - + -
30E LYS* 4.4 14.6 - - + +
31E ALA 3.6 24.0 - - - +
32E PHE* 4.1 16.4 - - + -
33E SER 3.0 23.3 + - - +
34E PRO 3.0 0.6 + - - -
35E GLU* 1.3 77.9 - - - +
37E ILE* 1.3 70.3 + - + +
39E MET* 3.5 6.7 + - - +
40E PHE* 3.0 23.2 + - - +
138E LEU* 4.7 10.3 - - + -
142E VAL* 4.1 17.3 - - + -
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Residues in contact with ILE 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ARG* 3.5 15.3 - - - +
34E PRO* 3.1 13.1 + - + +
36E VAL* 1.3 78.7 - - + +
38E PRO* 1.4 74.3 - - + +
40E PHE* 2.9 17.3 + - - +
41E SER* 3.1 15.8 + - - +
135E ILE* 3.8 31.2 - - + -
138E LEU* 4.0 22.4 - - + -
139E ASN* 3.3 38.8 - - - +
142E VAL* 4.2 9.0 - - + -
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Residues in contact with PRO 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E PRO 3.4 9.2 - - - +
35E GLU* 3.4 15.3 - - - +
37E ILE* 1.4 95.9 - - + +
39E MET* 1.3 56.9 + - + +
41E SER* 3.2 8.4 + - - +
42E ALA* 2.7 31.9 + - - +
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Residues in contact with MET 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ALA* 6.2 1.1 - - - -
23E TRP* 5.1 1.1 - - + -
26E VAL* 4.2 35.2 - - + -
35E GLU* 3.5 14.6 + - + +
36E VAL 3.7 8.5 - - - +
37E ILE 3.1 0.8 - - - -
38E PRO* 1.3 83.1 - - + +
40E PHE* 1.3 62.1 + - - +
42E ALA* 3.2 10.5 + - + +
43E LEU* 2.9 48.6 + - + +
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Residues in contact with PHE 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E TRP* 3.6 29.8 - + + -
36E VAL 3.0 12.6 + - - +
37E ILE 2.9 10.0 + - - +
39E MET* 1.3 76.5 - - - +
41E SER* 1.3 54.0 + - - +
43E LEU* 3.3 2.5 + - - +
44E SER* 2.6 46.9 + - - -
52E LEU* 4.0 20.9 - - + -
55E MET* 3.8 28.5 - - + -
56E LEU* 4.2 17.9 - - + -
131E LYS* 3.9 18.2 - - + -
134E ILE* 3.6 31.4 - - + -
135E ILE* 4.1 16.2 - - + -
138E LEU* 3.9 15.9 - - + -
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Residues in contact with SER 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ILE* 3.1 15.1 + - - +
38E PRO* 3.7 8.1 - - - +
40E PHE* 1.3 81.0 - - - +
42E ALA* 1.3 65.4 + - - +
44E SER* 3.6 10.4 + - - -
45E GLU* 3.8 18.7 + - - +
131E LYS* 4.0 9.9 + - - -
135E ILE* 3.5 24.5 - - - +
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Residues in contact with ALA 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E PRO 2.7 22.0 + - - +
39E MET* 3.6 16.2 - - + +
41E SER* 1.3 76.2 - - - +
43E LEU* 1.3 65.3 + - + +
44E SER 3.4 0.3 + - - -
45E GLU* 3.7 27.2 + - - +
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Residues in contact with LEU 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ILE* 5.0 4.7 - - - +
19E THR* 3.8 33.8 - - + +
22E ALA* 4.4 14.4 - - + -
23E TRP* 3.8 45.3 - - + +
26E VAL* 4.9 0.7 - - + -
39E MET* 2.9 40.0 + - + +
40E PHE 3.9 0.2 - - - +
42E ALA* 1.3 78.1 - - + +
44E SER* 1.3 58.8 + - - +
45E GLU 3.5 2.1 + - - +
55E MET* 3.9 18.1 - - + +
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Residues in contact with SER 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E PHE* 2.6 30.9 + - - -
41E SER 3.8 0.3 + - - -
42E ALA 3.3 1.0 - - - -
43E LEU* 1.3 77.5 - - - +
45E GLU* 1.3 60.6 + - - +
47E ALA* 3.1 22.7 + - - +
52E LEU* 3.5 24.9 - - - -
55E MET* 3.7 15.5 - - - -
131E LYS* 2.7 35.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il